kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

Bioinformatics

Volumn 31, Issue 17, 2015, Pages 2877-2878

  Gardner, Shea N ^a   Slezak, Tom ^a   Hall, Barry G ^b  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b Bellingham Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; ESCHERICHIA COLI; GENETICS; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PHYLOGENY; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; ESCHERICHIA COLI; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84940755707     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv271     Document Type: Article

References (8)

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3. Forde B.M., et al. (2014). The complete genome sequence of Escherichia coli Ec958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b: H4-St131 clone. Plos One, 9, E104400
4. Gardner S.N., and Hall B.G. (2013). When whole-genome alignments just won't work: Ksnp V2 Software for alignment-free Snp discovery, and phylogenetics of hundreds of microbial genomes. Plos One, 8, e81760
5. Hall B.G. (2014). Snp-associations, and phenotype predictions from hundreds of microbial genomes without genome alignments. Plos One, 9, E90490
6. Raphael B.H., et al. (2014). Distinguishing highly-related outbreak-associated Clostridium botulinum type A(B) strains. BMC Microbiol., 14, 192
7. Smith T.J., et al. (2015). Genomic sequences of six Botulinum neurotoxinproducing strains representing three Clostridial species illustrate the mobility, and diversity of Botulinum neurotoxin genes. Infect. Genet. Evol., 30, 102-113
8. Treangen T.J., et al. (2014). The harvest suite for rapid core-genome alignment, and visualization of thousands of intraspecific microbial genomes. Genome Biol., 15, 524